Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 110 of 226
Found at i:37748996 original size:20 final size:20
Alignment explanation
Indices: 37748973--37749020 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
37748963 AGACGAGATG
37748973 AATGAACTAAAGATGAGCTC
1 AATGAACTAAAGATGAGCTC
** * *
37748993 AATGAACTATGGTTGAGCTG
1 AATGAACTAAAGATGAGCTC
37749013 AATGAACT
1 AATGAACT
37749021 TGAAGTAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (20 bp):
AATGAACTAAAGATGAGCTC
Found at i:37758762 original size:10 final size:11
Alignment explanation
Indices: 37758739--37758777 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
37758729 AAAAAAAGGG
* *
37758739 AAAAAATTTGA
1 AAAAAAATTCA
37758750 AAAAAAATT-A
1 AAAAAAATTCA
37758760 AAAAAAATTCA
1 AAAAAAATTCA
37758771 AAAAAAA
1 AAAAAAA
37758778 AATTTGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:37761336 original size:22 final size:22
Alignment explanation
Indices: 37761293--37761357 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
37761283 CCTTTTTGAA
*
37761293 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAAAT
**
37761316 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* * *
37761338 CCCTTACCGTTTCATACCAA
1 CCATTACCATTTCGTACCAA
37761358 TTCCCAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:37768321 original size:22 final size:22
Alignment explanation
Indices: 37768290--37768354 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
37768280 ACCTTTTTGA
*
37768290 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
37768313 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
37768335 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
37768355 TTCCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:37771602 original size:28 final size:28
Alignment explanation
Indices: 37771571--37771637 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
37771561 CGGCTATGAC
*
37771571 TTAGACATCATTAA-AGCATGTAATAAAA
1 TTAGACA-CATTAATAACATGTAATAAAA
37771599 TTAGACACATTAATAACATGTAATAAAA
1 TTAGACACATTAATAACATGTAATAAAA
* *
37771627 TAAAACACATT
1 TTAGACACATT
37771638 TATCACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 6 0.17
28 29 0.83
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.28
Consensus pattern (28 bp):
TTAGACACATTAATAACATGTAATAAAA
Found at i:37773186 original size:18 final size:18
Alignment explanation
Indices: 37773160--37773211 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
37773150 TTGGAGAAAT
* *
37773160 AAAATAAAAAGACATTGA
1 AAAAGAAAAAGAAATTGA
*
37773178 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATTGA
*
37773196 AAAAGAAAAGGAAATT
1 AAAAGAAAAAGAAATT
37773212 ACAAAAGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.13
Consensus pattern (18 bp):
AAAAGAAAAAGAAATTGA
Found at i:37773216 original size:18 final size:18
Alignment explanation
Indices: 37773160--37773218 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
37773150 TTGGAGAAAT
* *
37773160 AAAATAAAAAGACATTGA-
1 AAAAGAAAAAGAAATT-AC
*
37773178 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATTAC
*
37773196 AAAAGAAAAGGAAATTAC
1 AAAAGAAAAAGAAATTAC
37773214 AAAAG
1 AAAAG
37773219 TGAGTGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.68, C:0.05, G:0.15, T:0.12
Consensus pattern (18 bp):
AAAAGAAAAAGAAATTAC
Found at i:37786778 original size:20 final size:20
Alignment explanation
Indices: 37786753--37786800 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
37786743 TCCATGCAGT
* *
37786753 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACACCAGCTCAAG
* *
37786773 TCAGCTCCCACCAGCTCAAT
1 TCAGCTCACACCAGCTCAAG
37786793 TCAGCTCA
1 TCAGCTCA
37786801 TTGAGCTCGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.21
Consensus pattern (20 bp):
TCAGCTCACACCAGCTCAAG
Found at i:37791270 original size:21 final size:21
Alignment explanation
Indices: 37791244--37791305 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
37791234 TTGGTATTTG
*
37791244 GGAATTGGTACGAAGTGGTAT
1 GGAATTGGTACGAAATGGTAT
*
37791265 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
37791286 GGTATTTGGTACGAATTGGT
1 GG-AATTGGTACGAAATGGT
37791306 CCAACACTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.27, C:0.03, G:0.35, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:37809888 original size:52 final size:52
Alignment explanation
Indices: 37809805--37809905 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
37809795 TAAGGAAACG
* * *
37809805 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
1 TAATAGACAGCAACTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
* *
37809857 TAATAGACAGCAACTTAAGACCTCCTTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAACTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAA
37809906 TATGTGCATG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAACTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
Found at i:37811538 original size:14 final size:15
Alignment explanation
Indices: 37811519--37811556 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
37811509 AACCGTATAT
37811519 AATTTTTTTCTTTC-
1 AATTTTTTTCTTTCG
37811533 AATTTTTTTCTTTCG
1 AATTTTTTTCTTTCG
37811548 AATTTTTTT
1 AATTTTTTT
37811557 TGTTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.71
Consensus pattern (15 bp):
AATTTTTTTCTTTCG
Found at i:37811582 original size:14 final size:13
Alignment explanation
Indices: 37811519--37811584 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 13
37811509 AACCGTATAT
37811519 AATTTTTTTCTTTC
1 AATTTTTTT-TTTC
37811533 AATTTTTTTCTTTC
1 AATTTTTTT-TTTC
37811547 GAATTTTTTTTGTT-
1 -AATTTTTTTT-TTC
*
37811561 -TTTGTTTTTTTTC
1 AATT-TTTTTTTTC
37811574 AAATTTTTTTT
1 -AATTTTTTTT
37811585 CGAACTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
12 4 0.09
13 6 0.14
14 21 0.48
15 13 0.30
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.74
Consensus pattern (13 bp):
AATTTTTTTTTTC
Found at i:37811595 original size:27 final size:27
Alignment explanation
Indices: 37811523--37811596 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
37811513 GTATATAATT
*
37811523 TTTTTCTTTC-AATTTTTTTCTTTCGAA
1 TTTTT-TTTCGAATTTTTTTCTTTCAAA
** *
37811550 TTTTTTTT-GTTTTTGTTTTTTTTCAAA
1 TTTTTTTTCGAATTT-TTTTCTTTCAAA
37811577 TTTTTTTTCGAACTTTTTTT
1 TTTTTTTTCGAA-TTTTTTT
37811597 ACGTACCTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
26 6 0.16
27 23 0.62
28 5 0.14
29 3 0.08
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.73
Consensus pattern (27 bp):
TTTTTTTTCGAATTTTTTTCTTTCAAA
Found at i:37811921 original size:21 final size:21
Alignment explanation
Indices: 37811895--37811957 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37811885 TTGGTATTTG
37811895 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
37811916 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
37811937 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
37811958 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:37813148 original size:30 final size:30
Alignment explanation
Indices: 37813090--37813148 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
37813080 TTGAAAAGGT
* *
37813090 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
37813120 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
37813149 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:37818854 original size:14 final size:14
Alignment explanation
Indices: 37818835--37818888 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
37818825 ACTAGCTCTC
37818835 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
37818849 TTTTTTTTCA-AAT
1 TTTTTTTTCACAAT
*
37818862 TTTTTTTTCAAAAT
1 TTTTTTTTCACAAT
37818876 TTTTTTTTCACAA
1 TTTTTTTTCACAA
37818889 CTTGATATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
13 13 0.34
14 25 0.66
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:37818943 original size:11 final size:11
Alignment explanation
Indices: 37818927--37818968 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
37818917 GGAAACTAGT
37818927 TTTTTTTTGAA
1 TTTTTTTTGAA
37818938 TTTTTTTTGAA
1 TTTTTTTTGAA
*
37818949 TTTTTTTTCGAG
1 TTTTTTTT-GAA
37818961 TTTTTTTT
1 TTTTTTTT
37818969 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:37818969 original size:12 final size:12
Alignment explanation
Indices: 37818924--37818972 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
37818914 AATGGAAACT
*
37818924 AGTTTTTTTTTG
1 AGTTTTTTTTCG
*
37818936 AATTTTTTTT-G
1 AGTTTTTTTTCG
*
37818947 AATTTTTTTTCG
1 AGTTTTTTTTCG
37818959 AGTTTTTTTTCG
1 AGTTTTTTTTCG
37818971 AG
1 AG
37818973 AAACTACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 11 0.32
12 23 0.68
ACGTcount: A:0.14, C:0.04, G:0.14, T:0.67
Consensus pattern (12 bp):
AGTTTTTTTTCG
Found at i:37822418 original size:41 final size:40
Alignment explanation
Indices: 37822373--37822480 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 40
37822363 AATTCGGCCA
* *
37822373 AACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGT-GCAGCATTAAATTCGTCCAGACACATTTAT
*
37822414 AACATGTAGTGGCAGCATTAAATTTGTCCAGACACATTTAT
1 AACATGTAGT-GCAGCATTAAATTCGTCCAGACACATTTAT
37822455 AACATGTAGTGACAGCATTAAATTCG
1 AACATGTAGTG-CAGCATTAAATTCG
37822481 ACATATTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.02
41 60 0.98
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (40 bp):
AACATGTAGTGCAGCATTAAATTCGTCCAGACACATTTAT
Found at i:37822473 original size:22 final size:22
Alignment explanation
Indices: 37822408--37822473 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 22
37822398 GTCCAGGCAT
*
37822408 ATTTATAACATGTAGTGGCAGC
1 ATTTATAACATGTAGTGACAGC
** ***
37822430 A-TTA-AATTTGTCCAGACA-C
1 ATTTATAACATGTAGTGACAGC
37822449 ATTTATAACATGTAGTGACAGC
1 ATTTATAACATGTAGTGACAGC
37822471 ATT
1 ATT
37822474 AAATTCGACA
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
19 2 0.07
20 11 0.37
21 12 0.40
22 5 0.17
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (22 bp):
ATTTATAACATGTAGTGACAGC
Found at i:37825084 original size:11 final size:11
Alignment explanation
Indices: 37825068--37825093 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
37825058 ATGTACAAAC
37825068 TAAAACATAAT
1 TAAAACATAAT
37825079 TAAAACATAAT
1 TAAAACATAAT
37825090 TAAA
1 TAAA
37825094 TACACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAACATAAT
Found at i:37829032 original size:122 final size:122
Alignment explanation
Indices: 37828815--37829060 Score: 483
Period size: 122 Copynumber: 2.0 Consensus size: 122
37828805 CGAACTCCAC
37828815 ATGAGGTAAGCAATCTTCCCAGATTTTCAAATTCTTTTGCAAAATAGCTCGAAGCAAAGTCGATA
1 ATGAGGTAAGCAATCTTCCCAGATTTTCAAATTCTTTTGCAAAATAGCTCGAAGCAAAGTCGATA
37828880 GCACACGGTTTACTACTTCGGTTTGGCCATCCGTTTGAGGGTGGCATGTCGTCGAAA
66 GCACACGGTTTACTACTTCGGTTTGGCCATCCGTTTGAGGGTGGCATGTCGTCGAAA
*
37828937 ATGAGGTAAGCAATCTTCCCATATTTTCAAATTCTTTTGCAAAATAGCTCGAAGCAAAGTCGATA
1 ATGAGGTAAGCAATCTTCCCAGATTTTCAAATTCTTTTGCAAAATAGCTCGAAGCAAAGTCGATA
37829002 GCACACGGTTTACTACTTCGGTTTGGCCATCCGTTTGAGGGTGGCATGTCGTCGAAA
66 GCACACGGTTTACTACTTCGGTTTGGCCATCCGTTTGAGGGTGGCATGTCGTCGAAA
37829059 AT
1 AT
37829061 ACAAGTTTGG
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 123 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (122 bp):
ATGAGGTAAGCAATCTTCCCAGATTTTCAAATTCTTTTGCAAAATAGCTCGAAGCAAAGTCGATA
GCACACGGTTTACTACTTCGGTTTGGCCATCCGTTTGAGGGTGGCATGTCGTCGAAA
Found at i:37831344 original size:14 final size:14
Alignment explanation
Indices: 37831325--37831355 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
37831315 NNNNNNNTCA
*
37831325 CTCTTTTTGTTTTT
1 CTCTTTTTCTTTTT
37831339 CTCTTTTTCTTTTT
1 CTCTTTTTCTTTTT
37831353 CTC
1 CTC
37831356 GCTCAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (14 bp):
CTCTTTTTCTTTTT
Found at i:37833448 original size:13 final size:13
Alignment explanation
Indices: 37833430--37833463 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
37833420 ATATATATAT
37833430 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
37833443 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
37833456 TTTTTTTT
1 TTTTTTTT
37833464 ACAATCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:37836851 original size:6 final size:6
Alignment explanation
Indices: 37836832--37836881 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
37836822 GGGCTCACAC
** * * *
37836832 TCTTTT TCAATT TCTTTT TCTTTT TCCTTT TCCTTT TCTATT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
37836880 TC
1 TC
37836882 AATTTTATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (6 bp):
TCTTTT
Found at i:37843128 original size:50 final size:50
Alignment explanation
Indices: 37843053--37843295 Score: 335
Period size: 50 Copynumber: 4.8 Consensus size: 50
37843043 ATTAGGGTAA
* * *
37843053 AGAGGCCCCATGTAAGACCATGTCTGGGACATGGGATTGGCATCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
37843103 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAA-ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACC-AAGATG
* * *
37843153 AGAGGTCCTATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * * *
37843203 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** *
37843253 AGTACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
37843296 TGTTATTATC
Statistics
Matches: 172, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 135 0.78
51 36 0.21
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:37847913 original size:4 final size:4
Alignment explanation
Indices: 37847904--37847938 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
37847894 AAGTTTTATT
37847904 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
37847939 TACTTAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:37852850 original size:20 final size:20
Alignment explanation
Indices: 37852827--37852872 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
37852817 GGGGTAAAAT
*
37852827 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
37852847 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
37852867 TGAGCT
1 TGAGCT
37852873 AGAAACGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:37854338 original size:10 final size:10
Alignment explanation
Indices: 37854323--37854384 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
37854313 TTTGAACCAT
*
37854323 TACCAATTCG
1 TACCAATTCA
*
37854333 TACCAAATACCA
1 TACC-AAT-TCA
*
37854345 TACCATTTCA
1 TACCAATTCA
37854355 TACCAATTCCA
1 TACCAATT-CA
* *
37854366 TACCATTTCG
1 TACCAATTCA
37854376 TACCAATTC
1 TACCAATTC
37854385 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37854368 original size:21 final size:21
Alignment explanation
Indices: 37854323--37854385 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37854313 TTTGAACCAT
* *
37854323 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37854345 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37854366 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37854386 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37854832 original size:27 final size:27
Alignment explanation
Indices: 37854802--37854872 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
37854792 AAAAAATTTG
*
37854802 AAAAAAAAAG-AAAAAAA-AAGTGAGCAA
1 AAAAAAAAAGTAAAAAAAGAAG-AAG-AA
*
37854829 AAAAAAAGAGTAAAAAAAGAAGAAGAA
1 AAAAAAAAAGTAAAAAAAGAAGAAGAA
*
37854856 AAAAAAAGAAGTGAAAA
1 AAAAAAA-AAGTAAAAA
37854873 GTCTTGCGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 18 0.49
28 16 0.43
29 3 0.08
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (27 bp):
AAAAAAAAAGTAAAAAAAGAAGAAGAA
Found at i:37854864 original size:13 final size:14
Alignment explanation
Indices: 37854802--37854866 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 14
37854792 AAAAAATTTG
37854802 AAAAAAA-AAG-AA
1 AAAAAAAGAAGCAA
*
37854814 AAAAAAAGTGAGCAA
1 AAAAAAAG-AAGCAA
*
37854829 AAAAAAAG-AGTAA
1 AAAAAAAGAAGCAA
37854842 AAAAAGAAGAAG-AA
1 AAAAA-AAGAAGCAA
37854856 AAAAAAAGAAG
1 AAAAAAAGAAG
37854867 TGAAAAGTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
12 7 0.15
13 15 0.33
14 12 0.26
15 12 0.26
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAGCAA
Found at i:37857086 original size:21 final size:22
Alignment explanation
Indices: 37857033--37857100 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 22
37857023 CCATTTTGAA
* *
37857033 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAATT
*
37857056 CCATTACCATTTCATACCAATT
1 CCATTACCATTTCGTACCAATT
37857078 CCA-TACCATTTCGTACCAATT
1 CCATTACCATTTCGTACCAATT
37857099 CC
1 CC
37857101 CAAATACCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.46
22 14 0.34
23 8 0.20
ACGTcount: A:0.28, C:0.34, G:0.03, T:0.35
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAATT
Found at i:37857288 original size:4 final size:4
Alignment explanation
Indices: 37857279--37857309 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
37857269 AAGTTTTATT
37857279 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
37857310 TACTTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:37863087 original size:20 final size:19
Alignment explanation
Indices: 37863062--37863099 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
37863052 AACATTTTTG
37863062 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
*
37863082 ATTCAGTTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
37863100 GTTATTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:37864827 original size:14 final size:14
Alignment explanation
Indices: 37864810--37864855 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
37864800 AAATATATAT
37864810 AAAAAAATTCAAAA
1 AAAAAAATTCAAAA
****
37864824 AAAAAAATTTTTGA
1 AAAAAAATTCAAAA
37864838 AAAAAAATTCAAAA
1 AAAAAAATTCAAAA
37864852 AAAA
1 AAAA
37864856 GTTTGTATTC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (14 bp):
AAAAAAATTCAAAA
Found at i:37864944 original size:30 final size:30
Alignment explanation
Indices: 37864902--37864973 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
37864892 TATTGAAGAA
**
37864902 AAAAAAAGAAGAAGAAAAAAAATTCGGAATT-
1 AAAAAAA-AAGAAGAAAAAAAA-TCAAAATTG
37864933 AAAAAAAAAGAAGAAAAAAAATCAAAATTG
1 AAAAAAAAAGAAGAAAAAAAATCAAAATTG
37864963 AAAAAAAAAGA
1 AAAAAAAAAGA
37864974 GTGATTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 6 0.16
30 25 0.66
31 7 0.18
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (30 bp):
AAAAAAAAAGAAGAAAAAAAATCAAAATTG
Found at i:37867369 original size:20 final size:19
Alignment explanation
Indices: 37867344--37867381 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
37867334 AACATTTTTG
37867344 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
*
37867364 ATTCAGTTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
37867382 GTTATTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:37870189 original size:15 final size:14
Alignment explanation
Indices: 37870153--37870207 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
37870143 TCTCTTGAGC
37870153 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
37870167 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
37870181 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
37870196 GAAAGAAAAGAA
1 GAGA-AAAAGAA
37870208 TGATGAGAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:37883651 original size:19 final size:18
Alignment explanation
Indices: 37883615--37883654 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
37883605 TTTCCACTCG
*
37883615 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
37883633 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
37883652 TTT
1 TTT
37883655 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:37884718 original size:13 final size:13
Alignment explanation
Indices: 37884675--37884705 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
37884665 CTAGCAATCT
*
37884675 TTTTTTTTCACAA
1 TTTTTTTTCAAAA
37884688 TTTTTTTTCAAAA
1 TTTTTTTTCAAAA
37884701 TTTTT
1 TTTTT
37884706 AAAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTTTCAAAA
Found at i:37884781 original size:13 final size:13
Alignment explanation
Indices: 37884763--37884809 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
37884753 GGAAACTAGT
37884763 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
*
37884776 -TTTTTTTTGAAA
1 TTTTTTTTTCAAA
*
37884788 TATTTTTTTTCAAG
1 T-TTTTTTTTCAAA
37884802 TTTTTTTT
1 TTTTTTTT
37884810 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 11 0.38
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:37884781 original size:14 final size:14
Alignment explanation
Indices: 37884762--37884809 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
37884752 TGGAAACTAG
37884762 TTTTTTTTTTCAAA
1 TTTTTTTTTTCAAA
*
37884776 --TTTTTTTTGAAA
1 TTTTTTTTTTCAAA
* *
37884788 TATTTTTTTTCAAG
1 TTTTTTTTTTCAAA
37884802 TTTTTTTT
1 TTTTTTTT
37884810 CGAGAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 11 0.39
14 17 0.61
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTTCAAA
Found at i:37886790 original size:22 final size:22
Alignment explanation
Indices: 37886726--37886792 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
37886716 CTGTTACAAC
**
37886726 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGTT
37886748 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
*
37886770 TCACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
37886792 T
1 T
37886793 GAACAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGTT
Found at i:37888394 original size:18 final size:17
Alignment explanation
Indices: 37888371--37888442 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 17
37888361 TCTTCACTCG
*
37888371 TTTCTTTTACAGACTCTC
1 TTTCTTTTTCA-ACTCTC
**
37888389 TTTCTTTTTC-ACTCAA
1 TTTCTTTTTCAACTCTC
* *
37888405 TTTC-TTTTCAGGCTCTT
1 TTTCTTTTTCA-ACTCTC
37888422 TTTCTTTTTCAA-TCTC
1 TTTCTTTTTCAACTCTC
37888438 TTTCT
1 TTTCT
37888443 CCTTTTCACT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 5 0.12
16 16 0.37
17 7 0.16
18 15 0.35
ACGTcount: A:0.12, C:0.25, G:0.04, T:0.58
Consensus pattern (17 bp):
TTTCTTTTTCAACTCTC
Found at i:37888401 original size:33 final size:33
Alignment explanation
Indices: 37888363--37888432 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
37888353 GATTACTCTC
*
37888363 TTCACTC-GTTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCAATTTCTTTT-CAGACTCTCTTTCTTT
* *
37888396 TTCACTCAATTTCTTTTCAGGCTCTTTTTCTTT
1 TTCACTCAATTTCTTTTCAGACTCTCTTTCTTT
37888429 TTCA
1 TTCA
37888433 ATCTCTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.13, C:0.26, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCAATTTCTTTTCAGACTCTCTTTCTTT
Found at i:37889680 original size:19 final size:18
Alignment explanation
Indices: 37889656--37889709 Score: 81
Period size: 19 Copynumber: 2.9 Consensus size: 18
37889646 AAAATAAACT
37889656 TTTTTTTGAATTTTTTTCA
1 TTTTTTTG-ATTTTTTTCA
37889675 TTTTTTTGATTTTTTTCA
1 TTTTTTTGATTTTTTTCA
*
37889693 TTTTTTTTCATTTTTTT
1 -TTTTTTTGATTTTTTT
37889710 TCACAATGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 10 0.30
19 23 0.70
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.80
Consensus pattern (18 bp):
TTTTTTTGATTTTTTTCA
Found at i:37889690 original size:9 final size:9
Alignment explanation
Indices: 37889665--37889709 Score: 72
Period size: 9 Copynumber: 4.9 Consensus size: 9
37889655 TTTTTTTTGA
37889665 ATTTTTTTC
1 ATTTTTTTC
*
37889674 ATTTTTTTG
1 ATTTTTTTC
37889683 ATTTTTTTC
1 ATTTTTTTC
37889692 ATTTTTTTTC
1 A-TTTTTTTC
37889702 ATTTTTTT
1 ATTTTTTT
37889710 TCACAATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 24 0.73
10 9 0.27
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:37889710 original size:10 final size:10
Alignment explanation
Indices: 37889655--37889712 Score: 75
Period size: 10 Copynumber: 6.0 Consensus size: 10
37889645 CAAAATAAAC
*
37889655 TTTTTTTTGA
1 TTTTTTTTCA
*
37889665 ATTTTTTTCA
1 TTTTTTTTCA
*
37889675 -TTTTTTTGA
1 TTTTTTTTCA
37889684 -TTTTTTTCA
1 TTTTTTTTCA
37889693 TTTTTTTTCA
1 TTTTTTTTCA
37889703 TTTTTTTTCA
1 TTTTTTTTCA
37889713 CAATGACTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.37
10 27 0.63
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:37890904 original size:22 final size:22
Alignment explanation
Indices: 37890852--37890906 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
37890842 TATTTGGGAA
* *
37890852 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAACGGTAAGAGAT
** * *
37890874 TTGAAACGAAATGGTAATAGAT
1 TTGGTACGAAACGGTAAGAGAT
37890896 TTGGTACGAAA
1 TTGGTACGAAA
37890907 ATGGAAATGG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.29, T:0.27
Consensus pattern (22 bp):
TTGGTACGAAACGGTAAGAGAT
Found at i:37893368 original size:20 final size:19
Alignment explanation
Indices: 37893337--37893374 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
37893327 TAATAATAAC
37893337 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
37893356 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
37893375 CAAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:37894882 original size:21 final size:20
Alignment explanation
Indices: 37894838--37894882 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
37894828 CAAATTCTTT
*
37894838 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
37894858 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
37894879 TTTC
1 TTTC
37894883 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:37895779 original size:28 final size:30
Alignment explanation
Indices: 37895738--37895805 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
37895728 CAATCACTCT
**
37895738 TTTTTTTTTCAATTTTG-ATTTTTTTCTTC
1 TTTTTTTTTCAATTACGAATTTTTTTCTTC
37895767 TTTTTTTTT-AATTACGAATTTTTTTCTTC
1 TTTTTTTTTCAATTACGAATTTTTTTCTTC
37895796 TTTTTTTTTC
1 TTTTTTTTTC
37895806 TTCAATACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 5 0.14
29 30 0.86
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (30 bp):
TTTTTTTTTCAATTACGAATTTTTTTCTTC
Found at i:37895867 original size:13 final size:13
Alignment explanation
Indices: 37895844--37895896 Score: 72
Period size: 13 Copynumber: 4.0 Consensus size: 13
37895834 AAATTGAATA
37895844 CAAACTTTTTTTTT
1 CAAA-TTTTTTTTT
*
37895858 -GAATTTTTTTTT
1 CAAATTTTTTTTT
37895870 CAAATTTTTTTTT
1 CAAATTTTTTTTT
37895883 CAAATTTTTATTTT
1 CAAATTTTT-TTTT
37895897 ATTTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 9 0.26
13 22 0.63
14 4 0.11
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.68
Consensus pattern (13 bp):
CAAATTTTTTTTT
Found at i:37898717 original size:20 final size:19
Alignment explanation
Indices: 37898688--37898725 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
37898678 AGCTAATAAC
37898688 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
37898707 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
37898726 CAAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:37904784 original size:2 final size:2
Alignment explanation
Indices: 37904777--37904823 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
37904767 CCCTCCCACT
*
37904777 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
37904819 TC TC T
1 TC TC T
37904824 ACACCCTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:37911205 original size:20 final size:20
Alignment explanation
Indices: 37911182--37911228 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
37911172 GGGTTGAGGT
37911182 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
37911202 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
37911222 TGAGCTG
1 TGAGCTG
37911229 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:37911833 original size:29 final size:29
Alignment explanation
Indices: 37911797--37911995 Score: 227
Period size: 29 Copynumber: 6.9 Consensus size: 29
37911787 GATGGTCAAA
* *
37911797 ACCATCCCTTTTCATATTCGATGGTTGCC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* * *
37911826 ACCGTCCCTTTTCTTATTCGATGGTTGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* *
37911855 ACCGTCCCTGTTCATATTCGATGGTCGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* *
37911884 AGCATCCCTTTTCATATTCGATGATCGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* * * **
37911913 ACCATTCCTTTTCAAATTCGATGGCCGAA
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* * * *
37911942 ACTAACCCTTTTCATATTTGATGGTTGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
*
37911971 AGCATCCCTTTTCATATTCGATGGT
1 ACCATCCCTTTTCATATTCGATGGT
37911996 GATCGAGGGT
Statistics
Matches: 140, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 140 1.00
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.39
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATGGTCGTC
Found at i:37915242 original size:8 final size:9
Alignment explanation
Indices: 37915224--37915250 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
37915214 CAATTCCTCC
37915224 TTTATTTTT
1 TTTATTTTT
37915233 TTTATTTTT
1 TTTATTTTT
37915242 TTTATTTTT
1 TTTATTTTT
37915251 GAATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTATTTTT
Found at i:37916428 original size:52 final size:52
Alignment explanation
Indices: 37916367--37916467 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
37916357 CATGCACATA
* *
37916367 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
37916419 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
37916468 CGTTTCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:37919882 original size:20 final size:20
Alignment explanation
Indices: 37919857--37919903 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
37919847 AGCTTGTTTC
37919857 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
37919877 CAGCTCATTCGAGTTGAATT
1 CAGCTCACTCGAGCTCAAGT
37919897 CAGCTCA
1 CAGCTCA
37919904 ACCTCAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:37936951 original size:30 final size:30
Alignment explanation
Indices: 37936912--37936968 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
37936902 AAACAAATTA
*
37936912 AATTCGGACATATTTAATAATATCTAAACT
1 AATTAGGACATATTTAATAATATCTAAACT
37936942 AATTAGGACATATTTAATAATATCTAA
1 AATTAGGACATATTTAATAATATCTAA
37936969 TTATTGTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (30 bp):
AATTAGGACATATTTAATAATATCTAAACT
Found at i:37942210 original size:16 final size:16
Alignment explanation
Indices: 37942189--37942231 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
37942179 GACCGTATAT
37942189 AATTTTTTTTCTTTTC
1 AATTTTTTTTCTTTTC
*
37942205 AATTTTTTTTCTTTTG
1 AATTTTTTTTCTTTTC
*
37942221 ATTTTTTTTTC
1 AATTTTTTTTC
37942232 AATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (16 bp):
AATTTTTTTTCTTTTC
Found at i:37942254 original size:14 final size:13
Alignment explanation
Indices: 37942193--37942255 Score: 65
Period size: 13 Copynumber: 4.6 Consensus size: 13
37942183 GTATATAATT
37942193 TTTTTTCTTTTCAA
1 TTTTTT-TTTTCAA
**
37942207 TTTTTTTTCTTTTGA
1 -TTTTTTT-TTTCAA
37942222 -TTTTTTTTTCAA
1 TTTTTTTTTTCAA
37942234 TTTTTTTTTTCAAA
1 TTTTTTTTTTC-AA
37942248 TTTTTTTT
1 TTTTTTTT
37942256 CAGAAATCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 4 0.10
13 16 0.39
14 11 0.27
15 10 0.24
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:37943469 original size:29 final size:29
Alignment explanation
Indices: 37943435--37943507 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 29
37943425 ATGTATTAGT
*
37943435 TTAGGACATATTTAAAAC-ACTTGAACTAA
1 TTAGGACATATTTAAAACAAC-TAAACTAA
37943464 TTAGGACATATTTAAAACAACTAAACTAA
1 TTAGGACATATTTAAAACAACTAAACTAA
37943493 TTAGGACATATTTAA
1 TTAGGACATATTTAA
37943508 TAATATCTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 40 0.95
30 2 0.05
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACAACTAAACTAA
Found at i:37945544 original size:12 final size:12
Alignment explanation
Indices: 37945527--37945569 Score: 70
Period size: 11 Copynumber: 3.6 Consensus size: 12
37945517 GAATACAAAC
37945527 TTTTTTTCGAAT
1 TTTTTTTCGAAT
37945539 TTTTTTTCGAAAT
1 TTTTTTTCG-AAT
37945552 TTTTTTT-GAAT
1 TTTTTTTCGAAT
37945563 TTTTTTT
1 TTTTTTT
37945570 ACAATCTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.33
12 10 0.33
13 10 0.33
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:37950344 original size:21 final size:21
Alignment explanation
Indices: 37950306--37950347 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
37950296 TTTTTTGCTC
*
37950306 GATTTTTTTTCACTTTTTTTT
1 GATTTTTTTTCACGTTTTTTT
**
37950327 GATTTTTTTTTTCGTTTTTTT
1 GATTTTTTTTCACGTTTTTTT
37950348 TAAACCAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (21 bp):
GATTTTTTTTCACGTTTTTTT
Found at i:37950430 original size:10 final size:10
Alignment explanation
Indices: 37950415--37950445 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
37950405 TACAACTCGA
37950415 GATTTTTTTT
1 GATTTTTTTT
37950425 GATTTTTTTTT
1 GA-TTTTTTTT
37950436 GATTTTTTTT
1 GATTTTTTTT
37950446 ACAAACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (10 bp):
GATTTTTTTT
Found at i:37950433 original size:11 final size:11
Alignment explanation
Indices: 37950417--37950445 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
37950407 CAACTCGAGA
37950417 TTTTTTTTGAT
1 TTTTTTTTGAT
37950428 TTTTTTTTGAT
1 TTTTTTTTGAT
37950439 TTTTTTT
1 TTTTTTT
37950446 ACAAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:37953040 original size:108 final size:108
Alignment explanation
Indices: 37952851--37953067 Score: 425
Period size: 108 Copynumber: 2.0 Consensus size: 108
37952841 AACGCTCAAT
37952851 GCCTTTTTTCCCTCACAATTTCTCGTGTTTTTAGTTCTTTAAAGGACTAATCCAACATTTCAGAA
1 GCCTTTTTTCCCTCACAATTTCTCGTGTTTTTAGTTCTTTAAAGGACTAATCCAACATTTCAGAA
*
37952916 CCTGTTATAATTGTGTTGGCTATAAGGAAAACGCACGGTTAGA
66 CCTGTTATAATTGTGTTGGCTATAAGGAAAACACACGGTTAGA
37952959 GCCTTTTTTCCCTCACAATTTCTCGTGTTTTTAGTTCTTTAAAGGACTAATCCAACATTTCAGAA
1 GCCTTTTTTCCCTCACAATTTCTCGTGTTTTTAGTTCTTTAAAGGACTAATCCAACATTTCAGAA
37953024 CCTGTTATAATTGTGTTGGCTATAAGGAAAACACACGGTTAGA
66 CCTGTTATAATTGTGTTGGCTATAAGGAAAACACACGGTTAGA
37953067 G
1 G
37953068 AGAGAAAAAA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (108 bp):
GCCTTTTTTCCCTCACAATTTCTCGTGTTTTTAGTTCTTTAAAGGACTAATCCAACATTTCAGAA
CCTGTTATAATTGTGTTGGCTATAAGGAAAACACACGGTTAGA
Found at i:37953134 original size:19 final size:19
Alignment explanation
Indices: 37953095--37953134 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
37953085 GAACAAAGGG
* *
37953095 AAAGGATAAGAAAAGAGTA
1 AAAGGATAAGAAAAAAATA
37953114 AAAGGATAAGAAAAAAATA
1 AAAGGATAAGAAAAAAATA
37953133 AA
1 AA
37953135 CAAAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAGGATAAGAAAAAAATA
Found at i:37954562 original size:52 final size:52
Alignment explanation
Indices: 37954484--37954584 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
37954474 CATGCACATA
* * *
37954484 TTTGAGCTTCAACCGAGCGAGAAATGAGGTCTTAAGCTACTGTCTATTATTG
1 TTTGAGCTTCAACCAAGCGAGAAATGAGATCTTAAGCTACTGTCCATTATTG
* * * *
37954536 TTTGAGCTTCAACTAAGCTAGAAATGAGATTTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCAAGCGAGAAATGAGATCTTAAGCTACTGTCCATTA
37954585 CGTTTCCTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (52 bp):
TTTGAGCTTCAACCAAGCGAGAAATGAGATCTTAAGCTACTGTCCATTATTG
Found at i:37956946 original size:41 final size:40
Alignment explanation
Indices: 37956884--37956962 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 40
37956874 GAATAAGAAT
* *
37956884 TTGATACGGCCCGGCCTCGTTGATGAATCCGAGTCGTTGA
1 TTGATACGCCCCGGCCGCGTTGATGAATCCGAGTCGTTGA
37956924 TTGATACGACCCCGGCCGCGTTGATGAATCCGAGTCGTT
1 TTGATACG-CCCCGGCCGCGTTGATGAATCCGAGTCGTT
37956963 TTCGTTGCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 8 0.22
41 28 0.78
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (40 bp):
TTGATACGCCCCGGCCGCGTTGATGAATCCGAGTCGTTGA
Found at i:37958071 original size:29 final size:29
Alignment explanation
Indices: 37958037--37958109 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 29
37958027 ATGTATTAGT
*
37958037 TTAGGACATATTTAAAAC-ACTTGAACTAA
1 TTAGGACATATTTAAAACAAC-TAAACTAA
37958066 TTAGGACATATTTAAAACAACTAAACTAA
1 TTAGGACATATTTAAAACAACTAAACTAA
37958095 TTAGGACATATTTAA
1 TTAGGACATATTTAA
37958110 TAATATCTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 40 0.95
30 2 0.05
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACAACTAAACTAA
Found at i:37965659 original size:31 final size:31
Alignment explanation
Indices: 37965621--37965683 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
37965611 AAATTACAAG
37965621 AGTAATTGAATCCTAAT-AAAACTCTTTCAAA
1 AGTAATTGAATCCTAATAAAAACTCTTT-AAA
37965652 AGTAATTGAATCCTAATAAAAACTCTTTAAA
1 AGTAATTGAATCCTAATAAAAACTCTTTAAA
37965683 A
1 A
37965684 TTATCTAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (31 bp):
AGTAATTGAATCCTAATAAAAACTCTTTAAA
Found at i:37968786 original size:21 final size:20
Alignment explanation
Indices: 37968759--37968812 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
37968749 AGGTAGGCAA
37968759 CTTTTTTTTTGC-GCTTTTTG
1 CTTTTTTTTTGCTG-TTTTTG
37968779 CTCTTTTTTTTGCTGTTTTTG
1 CT-TTTTTTTTGCTGTTTTTG
37968800 CTTTTTTTTTGCT
1 CTTTTTTTTTGCT
37968813 TTTATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.41
21 18 0.56
22 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.13, T:0.72
Consensus pattern (20 bp):
CTTTTTTTTTGCTGTTTTTG
Found at i:37968813 original size:11 final size:11
Alignment explanation
Indices: 37968773--37968815 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
37968763 TTTTTTGCGC
37968773 TTTTTGCTCTTT
1 TTTTTGCT-TTT
*
37968785 TTTTTGC--TG
1 TTTTTGCTTTT
37968794 TTTTTGCTTTT
1 TTTTTGCTTTT
37968805 TTTTTGCTTTT
1 TTTTTGCTTTT
37968816 ATTTAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 8 0.30
11 12 0.44
12 7 0.26
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.77
Consensus pattern (11 bp):
TTTTTGCTTTT
Found at i:37973666 original size:20 final size:20
Alignment explanation
Indices: 37973643--37973699 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
37973633 GGGTTAAAAT
*
37973643 TGAGCTGAATTGATCTCAAA
1 TGAGCTGAATTGAGCTCAAA
* *
37973663 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAA
*
37973683 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
37973700 AAACAGAGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAA
Found at i:37975652 original size:21 final size:22
Alignment explanation
Indices: 37975563--37975647 Score: 86
Period size: 21 Copynumber: 3.9 Consensus size: 22
37975553 TTTCCACTCG
37975563 ATTTC-TTTTCAAGCTCTCTTTCA
1 ATTTCTTTTTCAA--TCTCTTTCA
* * *
37975586 ATTTCGTTTTCCA-CTCTTTCT
1 ATTTCTTTTTCAATCTCTTTCA
* *
37975607 TTTTCTTTTTC-TTCTCTTTCA
1 ATTTCTTTTTCAATCTCTTTCA
37975628 ATTTCTTTTTCAATCTCTTT
1 ATTTCTTTTTCAATCTCTTT
37975648 TATTTTTGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 33 0.65
22 7 0.14
23 5 0.10
24 6 0.12
ACGTcount: A:0.12, C:0.25, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTCTTTTTCAATCTCTTTCA
Found at i:37975684 original size:15 final size:15
Alignment explanation
Indices: 37975661--37975707 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
37975651 TTTTGAAATC
37975661 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
37975676 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
37975691 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
37975707 T
1 T
37975708 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:37976770 original size:13 final size:13
Alignment explanation
Indices: 37976754--37976805 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
37976744 TTTTCACTTC
*
37976754 TTTTTTTCTTCTT
1 TTTTTTTCTCCTT
*
37976767 TTTTTTACTCCTTT
1 TTTTTTTCTCC-TT
37976781 TTTTTTTGCTCACTT
1 TTTTTTT-CTC-CTT
37976796 CTTTTTTTCT
1 -TTTTTTTCT
37976806 TTTTTTTCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 9 0.28
14 8 0.25
15 7 0.22
16 8 0.25
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTTTCTCCTT
Found at i:37976783 original size:15 final size:17
Alignment explanation
Indices: 37976761--37976803 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
37976751 TTCTTTTTTT
37976761 CTTCTTTTTTTTACTC-
1 CTTCTTTTTTTTACTCA
*
37976777 CTT-TTTTTTTTGCTCA
1 CTTCTTTTTTTTACTCA
37976793 CTTCTTTTTTT
1 CTTCTTTTTTT
37976804 CTTTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
16 6 0.25
17 7 0.29
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (17 bp):
CTTCTTTTTTTTACTCA
Found at i:37976800 original size:16 final size:15
Alignment explanation
Indices: 37976750--37976803 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
37976740 AGACTTTTCA
*
37976750 CTTCTTTTTTT-CTT
1 CTTCTTTTTTTACTC
37976764 C-T-TTTTTTTACTC
1 CTTCTTTTTTTACTC
* *
37976777 CTTTTTTTTTTGCTC
1 CTTCTTTTTTTACTC
37976792 ACTTCTTTTTTT
1 -CTTCTTTTTTT
37976804 CTTTTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 7 0.21
13 4 0.12
14 2 0.06
15 10 0.30
16 10 0.30
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (15 bp):
CTTCTTTTTTTACTC
Found at i:37976822 original size:40 final size:42
Alignment explanation
Indices: 37976747--37976826 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
37976737 GCAAGACTTT
** *
37976747 TCACTTCTTTTTTTCTTCTTTTTTTTACTCCTTTTTTTTTTGC
1 TCACTTCTTTTTTTCTTCTTTTTTCGAAT-CTTTTTTTTTTGC
37976790 TCACTTCTTTTTTTCTT-TTTTTTCGAAT-TTTTTTTTT
1 TCACTTCTTTTTTTCTTCTTTTTTCGAATCTTTTTTTTT
37976827 GAATTTTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 9 0.26
42 8 0.24
43 17 0.50
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (42 bp):
TCACTTCTTTTTTTCTTCTTTTTTCGAATCTTTTTTTTTTGC
Found at i:37979628 original size:22 final size:22
Alignment explanation
Indices: 37979576--37979640 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
37979566 TATTTGGGAA
* * *
37979576 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
37979598 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
37979620 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
37979641 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:37982278 original size:42 final size:42
Alignment explanation
Indices: 37982219--37982343 Score: 250
Period size: 42 Copynumber: 3.0 Consensus size: 42
37982209 AAATTCAAAG
37982219 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
37982261 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
37982303 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
37982344 CACACATATT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (42 bp):
GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
Found at i:37984581 original size:20 final size:20
Alignment explanation
Indices: 37984556--37984602 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
37984546 AGCTCGTTTC
37984556 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
37984576 CAGCTCATTCGAGTTGAATT
1 CAGCTCACTCGAGCTCAAGT
37984596 CAGCTCA
1 CAGCTCA
37984603 ACCTCAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:37988880 original size:13 final size:13
Alignment explanation
Indices: 37988853--37988885 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
37988843 AACTATGAAC
37988853 TTTTCTT-TCTTT
1 TTTTCTTCTCTTT
*
37988865 TTTTCTTCTTTTT
1 TTTTCTTCTCTTT
37988878 TTTTCTTC
1 TTTTCTTC
37988886 AATACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTCTCTTT
Found at i:37988946 original size:11 final size:11
Alignment explanation
Indices: 37988930--37988978 Score: 64
Period size: 12 Copynumber: 4.4 Consensus size: 11
37988920 ATAAACTTTC
37988930 TTTTGAATTTT
1 TTTTGAATTTT
37988941 TTTTGAATTTAT
1 TTTTGAATTT-T
*
37988953 TTTTCAAGTTTT
1 TTTTGAA-TTTT
37988965 TTTTG-ATTTT
1 TTTTGAATTTT
37988975 TTTT
1 TTTT
37988979 ACAATACCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 8 0.24
11 11 0.32
12 12 0.35
13 3 0.09
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.73
Consensus pattern (11 bp):
TTTTGAATTTT
Found at i:37989334 original size:23 final size:23
Alignment explanation
Indices: 37989308--37989370 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
37989298 TCGGTTTAGG
**
37989308 TTTGTTACGAAATGGTAGTGTGA
1 TTTGTTACGAAATGGTAGTACGA
*
37989331 TTTGGTT-CGAAATGGTATTACGA
1 TTT-GTTACGAAATGGTAGTACGA
*
37989354 TTTGGTACGAAATGGTA
1 TTTGTTACGAAATGGTA
37989371 ATGGTTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.06
23 29 0.85
24 3 0.09
ACGTcount: A:0.27, C:0.06, G:0.29, T:0.38
Consensus pattern (23 bp):
TTTGTTACGAAATGGTAGTACGA
Found at i:37992544 original size:6 final size:6
Alignment explanation
Indices: 37992533--37992559 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
37992523 TAGGAGTTTG
37992533 TTTAGT TTTAGT TTTAGT TTTAGT TTT
1 TTTAGT TTTAGT TTTAGT TTTAGT TTT
37992560 CTAATTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTAGT
Found at i:37997642 original size:29 final size:29
Alignment explanation
Indices: 37997605--37997677 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
37997595 TTAGATATTA
* *
37997605 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
37997634 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
37997663 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
37997678 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:37999353 original size:26 final size:27
Alignment explanation
Indices: 37999313--37999366 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
37999303 AGAAGAAGAA
**
37999313 AAAAAAATCGGAATT-AAAAAAAAAAG
1 AAAAAAATCAAAATTGAAAAAAAAAAG
37999339 AAAAAAATCAAAATTGAAAAAAAAAAG
1 AAAAAAATCAAAATTGAAAAAAAAAAG
37999366 A
1 A
37999367 GTGATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (27 bp):
AAAAAAATCAAAATTGAAAAAAAAAAG
Found at i:38000201 original size:21 final size:20
Alignment explanation
Indices: 38000172--38000217 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
38000162 AATCTTGAAT
*
38000172 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
38000193 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
38000213 GAAAA
1 GAAAA
38000218 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:38002383 original size:22 final size:22
Alignment explanation
Indices: 38002355--38002507 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
38002345 TTTATTGTTC
*
38002355 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
38002377 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
38002399 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
38002421 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
38002443 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
38002465 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
38002487 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
38002508 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:38010923 original size:14 final size:14
Alignment explanation
Indices: 38010904--38010957 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
38010894 AACTAGCTCT
38010904 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
*
38010918 TTTTTTTTTCAAAA
1 TTTTTTTTTCACAA
38010932 TTTTTTTTTCA-AA
1 TTTTTTTTTCACAA
38010945 -TTTTTTTTCACAA
1 TTTTTTTTTCACAA
38010958 CTTGATATCC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
12 10 0.26
13 4 0.11
14 24 0.63
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:38011012 original size:11 final size:11
Alignment explanation
Indices: 38010996--38011037 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
38010986 GGAAACTAGT
38010996 TTTTTTTTGAA
1 TTTTTTTTGAA
38011007 TTTTTTTTGAA
1 TTTTTTTTGAA
*
38011018 TTTTTTTTCGAG
1 TTTTTTTT-GAA
38011030 TTTTTTTT
1 TTTTTTTT
38011038 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:38011038 original size:12 final size:12
Alignment explanation
Indices: 38010993--38011041 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
38010983 AATGGAAACT
*
38010993 AGTTTTTTTTTG
1 AGTTTTTTTTCG
*
38011005 AATTTTTTTT-G
1 AGTTTTTTTTCG
*
38011016 AATTTTTTTTCG
1 AGTTTTTTTTCG
38011028 AGTTTTTTTTCG
1 AGTTTTTTTTCG
38011040 AG
1 AG
38011042 AAACTACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 11 0.32
12 23 0.68
ACGTcount: A:0.14, C:0.04, G:0.14, T:0.67
Consensus pattern (12 bp):
AGTTTTTTTTCG
Found at i:38015389 original size:19 final size:19
Alignment explanation
Indices: 38015349--38015394 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
38015339 CCTCCACCCC
*
38015349 TTCTATTTTTCTTTCTTTT
1 TTCTATTTTTCTTTCTTCT
38015368 TTCTATTTTTCTTGTC-TCT
1 TTCTATTTTTCTT-TCTTCT
38015387 TTCT-TTTT
1 TTCTATTTT
38015395 CAATCTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 19 0.76
20 2 0.08
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (19 bp):
TTCTATTTTTCTTTCTTCT
Found at i:38017423 original size:12 final size:13
Alignment explanation
Indices: 38017406--38017456 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
38017396 ACTAGCTCTC
*
38017406 TTTTTTTCACAATT
1 TTTTTTTCA-AAAT
38017420 TTTTTTTCAAAATTT
1 TTTTTTTCAAAA--T
*
38017435 TTTTTTTCAAATT
1 TTTTTTTCAAAAT
38017448 TTTTTTTCA
1 TTTTTTTCA
38017457 CAACTTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 12 0.36
14 9 0.27
15 12 0.36
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTCAAAAT
Found at i:38017426 original size:15 final size:14
Alignment explanation
Indices: 38017406--38017459 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
38017396 ACTAGCTCTC
38017406 TTTTTTTCACAATT
1 TTTTTTTCACAATT
*
38017420 TTTTTTTCAAAATTT
1 TTTTTTTCACAA-TT
38017435 TTTTTTTCA-AATT
1 TTTTTTTCACAATT
38017448 TTTTTTTCACAA
1 TTTTTTTCACAA
38017460 CTTGATATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
13 11 0.30
14 15 0.41
15 11 0.30
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:38017526 original size:11 final size:12
Alignment explanation
Indices: 38017499--38017541 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
38017489 GAAACTAGTT
*
38017499 TTTTTTTTCAAA
1 TTTTTTTTCGAA
*
38017511 TTTTTTTTTGAA
1 TTTTTTTTCGAA
*
38017523 TTTTTTTTCGAG
1 TTTTTTTTCGAA
38017535 TTTTTTT
1 TTTTTTT
38017542 CAAGAAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:38021545 original size:20 final size:21
Alignment explanation
Indices: 38021501--38021545 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
38021491 AAATTATGAA
*
38021501 CCAAGAATGATTTTTGATACT
1 CCAAGAATGATTTATGATACT
38021522 -CAAGAATG-TTTATGA-ACTT
1 CCAAGAATGATTTATGATAC-T
38021541 CCAAG
1 CCAAG
38021546 CCGAATCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 2 0.10
19 7 0.33
20 12 0.57
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CCAAGAATGATTTATGATACT
Found at i:38029134 original size:20 final size:19
Alignment explanation
Indices: 38029111--38029175 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
38029101 AAGCTCAAAC
38029111 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
38029131 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
38029151 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
38029171 GAGCT
1 GAGCT
38029176 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:38030204 original size:18 final size:17
Alignment explanation
Indices: 38030175--38030224 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
38030165 AAAATTCCAA
38030175 TACTTC-ACTTTTTTTT
1 TACTTCAACTTTTTTTT
38030191 ATAC-TCGAACTTTTTTTT
1 -TACTTC-AACTTTTTTTT
38030209 TACTTCAA-TTTTTTTT
1 TACTTCAACTTTTTTTT
38030225 CAATTACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.33
17 8 0.27
18 12 0.40
ACGTcount: A:0.18, C:0.16, G:0.02, T:0.64
Consensus pattern (17 bp):
TACTTCAACTTTTTTTT
Found at i:38030221 original size:17 final size:17
Alignment explanation
Indices: 38030174--38030224 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 17
38030164 AAAAATTCCA
*
38030174 ATACTTCACTTTTTTTT
1 ATACTTCAATTTTTTTT
38030191 ATAC-TCGAACTTTTTTTT
1 ATACTTC-AA-TTTTTTTT
38030209 -TACTTCAATTTTTTTT
1 ATACTTCAATTTTTTTT
38030225 CAATTACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.33
17 10 0.33
18 10 0.33
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.63
Consensus pattern (17 bp):
ATACTTCAATTTTTTTT
Found at i:38034524 original size:26 final size:25
Alignment explanation
Indices: 38034494--38034542 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
38034484 CAATAATTCA
38034494 GGGAATCAACACTTAGCAACCCCTCG
1 GGGAAT-AACACTTAGCAACCCCTCG
**
38034520 GGGAATAGGACTTAGCAACCCCT
1 GGGAATAACACTTAGCAACCCCT
38034543 TTAGAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (25 bp):
GGGAATAACACTTAGCAACCCCTCG
Found at i:38035633 original size:11 final size:12
Alignment explanation
Indices: 38035605--38035637 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
38035595 GCCGAAACGT
38035605 CGAAATTTTTCAA
1 CGAAA-TTTTCAA
38035618 CGAAATTTTC-A
1 CGAAATTTTCAA
38035629 CGAAATTTT
1 CGAAATTTT
38035638 TCTGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 5 0.25
13 5 0.25
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:38035638 original size:12 final size:13
Alignment explanation
Indices: 38035605--38035639 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
38035595 GCCGAAACGT
38035605 CGAAATTTTTCAA
1 CGAAATTTTTCAA
38035618 CGAAA-TTTTC-A
1 CGAAATTTTTCAA
38035629 CGAAATTTTTC
1 CGAAATTTTTC
38035640 TGTGAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 10 0.48
13 5 0.24
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (13 bp):
CGAAATTTTTCAA
Found at i:38042351 original size:20 final size:20
Alignment explanation
Indices: 38042326--38042372 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38042316 AGCTCATTTC
*
38042326 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
38042346 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
38042366 CAGCTCA
1 CAGCTCA
38042373 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:38042375 original size:10 final size:10
Alignment explanation
Indices: 38042316--38042375 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
38042306 AGCTCTGTTT
*
38042316 AGCTCATTTCC
1 AGCTCAATT-C
* *
38042327 AGCTCACTTG
1 AGCTCAATTC
*
38042337 AGCTCAAGTC
1 AGCTCAATTC
38042347 AGCTC-ATTC
1 AGCTCAATTC
*
38042356 GAGATCAATTC
1 -AGCTCAATTC
38042367 AGCTCAATT
1 AGCTCAATT
38042376 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:38044599 original size:27 final size:30
Alignment explanation
Indices: 38044537--38044605 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
38044527 TTCAACATCT
*
38044537 TTTTCTTTTTCAATTTTTTTTCTCAATCTCA
1 TTTTCTTTTTCAATTTTCTTTCTC-ATCTCA
*
38044568 ATTTCTTTTTCAATTTTCTTT-TC-T-TCA
1 TTTTCTTTTTCAATTTTCTTTCTCATCTCA
38044595 TTTTCTTTTTC
1 TTTTCTTTTTC
38044606 TCTCACTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
30 2 0.06
31 19 0.54
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTTCTTTTTCAATTTTCTTTCTCATCTCA
Found at i:38045563 original size:16 final size:16
Alignment explanation
Indices: 38045542--38045581 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
38045532 TACAACCTCT
38045542 TTTTTTTTAGGCACGA
1 TTTTTTTTAGGCACGA
* *
38045558 TTTTTTTT-TGCATGA
1 TTTTTTTTAGGCACGA
38045573 TTTTTTTTA
1 TTTTTTTTA
38045582 ATTCACGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65
Consensus pattern (16 bp):
TTTTTTTTAGGCACGA
Found at i:38064215 original size:18 final size:19
Alignment explanation
Indices: 38064172--38064215 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
38064162 TGAAAAATCA
*
38064172 AAAGAAAATGAGCAAGAAC
1 AAAGAAAATGAGAAAGAAC
*
38064191 AAA-AAAATGA-AAAGAAT
1 AAAGAAAATGAGAAAGAAC
38064208 AAAGAAAA
1 AAAGAAAA
38064216 CAGTGTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 11 0.50
19 3 0.14
ACGTcount: A:0.73, C:0.05, G:0.16, T:0.07
Consensus pattern (19 bp):
AAAGAAAATGAGAAAGAAC
Found at i:38068997 original size:14 final size:14
Alignment explanation
Indices: 38068978--38069004 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38068968 TACATTGGAC
38068978 AGATTCATGCATGT
1 AGATTCATGCATGT
38068992 AGATTCATGCATG
1 AGATTCATGCATG
38069005 GGAGATGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
AGATTCATGCATGT
Found at i:38070858 original size:20 final size:20
Alignment explanation
Indices: 38070833--38070879 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38070823 AGCTCATTTC
*
38070833 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
38070853 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
38070873 CAGCTCA
1 CAGCTCA
38070880 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:38070882 original size:10 final size:10
Alignment explanation
Indices: 38070823--38070882 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
38070813 AGCTCTGTTT
*
38070823 AGCTCATTTCC
1 AGCTCAATT-C
* *
38070834 AGCTCACTTG
1 AGCTCAATTC
*
38070844 AGCTCAAGTC
1 AGCTCAATTC
38070854 AGCTC-ATTC
1 AGCTCAATTC
*
38070863 GAGATCAATTC
1 -AGCTCAATTC
38070874 AGCTCAATT
1 AGCTCAATT
38070883 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:38083855 original size:17 final size:18
Alignment explanation
Indices: 38083833--38083873 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
38083823 CATTTCTTTT
38083833 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
38083850 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
38083868 T-TTTTG
1 TCTTTTG
38083874 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:38086151 original size:16 final size:16
Alignment explanation
Indices: 38086126--38086188 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
38086116 CCGTATGCAA
38086126 TTTT-TTTTCAATTTT
1 TTTTCTTTTCAATTTT
38086141 TTTTCTTTTCAATTTT
1 TTTTCTTTTCAATTTT
* *
38086157 TTTTC----GATTTTT
1 TTTTCTTTTCAATTTT
38086169 TTTTCTTTTCAATTTT
1 TTTTCTTTTCAATTTT
38086185 TTTT
1 TTTT
38086189 TCTATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.26
15 4 0.10
16 25 0.64
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTCAATTTT
Found at i:38086168 original size:28 final size:27
Alignment explanation
Indices: 38086123--38086200 Score: 120
Period size: 29 Copynumber: 2.8 Consensus size: 27
38086113 AGACCGTATG
*
38086123 CAATTTTTTTTCAATTTTTTTTCTTTT
1 CAATTTTTTTTCATTTTTTTTTCTTTT
38086150 CAATTTTTTTTCGATTTTTTTTTCTTTT
1 CAATTTTTTTTC-ATTTTTTTTTCTTTT
38086178 CAATTTTTTTTTCTATTTTTTTT
1 CAA-TTTTTTTTC-ATTTTTTTT
38086201 CGAATCTACA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 12 0.26
28 17 0.36
29 18 0.38
ACGTcount: A:0.13, C:0.10, G:0.01, T:0.76
Consensus pattern (27 bp):
CAATTTTTTTTCATTTTTTTTTCTTTT
Done.